A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages

The aims of the work were (1) to develop statistical tests to identify whether substitution takes place under a covariotide model in sequences used for phylogenetic inference and (2) to determine the influence of covariotide substitution on phylogenetic trees inferred for photosynthetic and other organisms. (Covariotide and covarion models are ones in which sites that are variable in some parts of the underlying tree are invariable in others and vice versa.) Two tests were developed. The first was a contingency test, and the second was an inequality test comparing the expected number of variable sites in two groups with the observed number. Application of these tests to 16S rDNA and tufA sequences from a range of nonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes and eukaryotes suggests the occurrence of a covariotide mechanism. The degree of support for partitioning of taxa in reconstructed trees involving these organisms was determined in the presence or absence of sites showing particular substitution patterns. This analysis showed that the support for splits between (1) photosynthetic eukaryotes and prokaryotes and (2) photosynthetic and nonphotosynthetic organisms could be accounted for by patterns arising from covariotide substitution. We show that the additional problem of compositional bias in sequence data needs to be considered in the context of patterns of covariotide/covarion substitution. We argue that while covariotide or covarion substitution may give rise to phylogenetically informative patterns in sequence data, this may not always be so.      

Oscillatory Transpiration and Water Uptake of Avena Plants IV. Transpiratory Response to Sine Shaped Light Cycles

The transpiration rate of individual 6-day-old oat plants was forced to oscillate by cyclic sine-shaped changes in the leaf irradiance (frequency 2 cycles h^?1, amplitude and average value 1.4 mW cm^?2, red light 620–800 nm). By means of a specially designed cuvette with three chambers the transpiration rate from three different segments of the leaf could be measured simultaneously. The leaf segments were illuminated individually and the illumination on each leaf segment could be modulated independently. The experiments showed that there was a strong correlation between the transpiration rates from the different leaf segments, dependent on a coupling mechanism in the plant. The coupling phenomenon disappeared when the root system was eliminated or when the water potential of the root medium was lowered. It was experimentally shown that CO₂ diffusion in the leaf could not be the primary cause for the coupling. Therefore the stomatal dependence on the leaf water potential was considered the most probable reason for the coupling. The frequency of the forcing light cycles could be linearly changed during an experiment and this swept-frequency technique was used to obtain a frequency response of one single oat plant. The technique made it also possible to study the strength of the coupling between different leaf segments.     

Characterisation of a Tunisian coastal lagoon through hyperspectral underwater irradiance

North African coastal lagoons are unique ecosystems that often suffer degradation due to human activities. Therefore, monitoring methods are required to identify stressors and assist with the management of these valuable and often understudied ecosystems. A synthetic indicator of water ecological quality would be desirable for regular monitoring of these ecosystems under pressure. In 2008 an optical procedure was developed and applied in Ghar El Melh, a Tunisian lagoon which has been increasingly impacted by pollutant loading, especially from agriculture. In situ hyperspectral irradiance was measured at several stations, from which the apparent optical properties (AOPs), namely the irradiance attenuation coefficient K(λ) and the reflectance ratio R(λ), were obtained in order to relate them to water composition, in terms of light-attenuating substances (LASs). The significant relationships observed between R and LAS values enabled the application of a hyperspectral optical classification, which effectively highlighted threatened sectors of the lagoon. The pattern of differing water quality across the lagoon system that was derived from the hyperspectral classification agreed well with that obtained from a conventional optical classification that included AOPs and LASs. We suggest that hyperspectral analysis and classification is a useful monitoring tool for the assessment of change in coastal lagoons, and perhaps also in other shallow-water ecosystems.     

Effects of environmental salinity on gill endothelin receptor expression in the killifish, Fundulus heteroclitus

We recently determined that rapid changes in environmental salinity alter endothelin-1 (EDN1) mRNA levels in the euryhaline killifish, Fundulus heteroclitus, so we hypothesized that EDN1 may be a local regulator of gill ion transport in teleost fishes. The purpose of the present study was to examine the effects of changes in environmental salinity on the gill endothelin receptors: EDNRA, EDNRB, and EDNRC. Using quantitative real-time PCR, we determined that after a fresh water (FW) to seawater (SW) transfer, there is a two to threefold increase in gill EDNRA and EDNRB mRNA levels. Likewise, we found a two to three fold increase in gill EDNRA and EDNRB protein concentration. In addition, killifish that have acclimated to FW for 30 days had significantly lower EDNRA mRNA and protein levels than SW killifish. ENDRA were immunolocalized to the mitochondrion-rich cells of the killifish gill, suggesting that EDN1 signaling cascades may affect MRC function. EDNRB were found throughout the gill vasculature and on lamellar pillar cells. We previously immunolocalized EDN1 to the pillar cell suggesting that EDN1 acts as an autocrine signaling molecule and potentially regulates pillar cell tone and lamellar perfusion. We conclude that EDN1 is physiologically active in the teleost gill, and regulated by environmental salinity. Future functional studies examining the physiological role of this system are necessary to completely understand EDN1 in the fish gill.     

Assembly of the sarcoplasmic reticulum proteins in differentiating rat skeletal muscle cell cultures: localization by immunofluorescence of sarcoplasmic reticulum proteins in differentiating rat skeletal muscle cell cultures

Immunofluorescent staining techniques were used to study the distribution of the Ca(2) + Mg(2+)-dependent ATPase and calsequestrin in primary cultures of differentiating rat skeletal muscle cells, grown for different periods of time under various culture conditions. In mononucleated myoblasts calsequestrin was detected after 45 h in culture whereas the ATPase was not detected until 60 h. After cell fusion began, both proteins could be identified in all multinucleated cells. Myoblasts grown for longer than 60 h in low Ca(2+) medium contained calsequestrin and the ATPase, even though they were unable to fuse. These studies at the cellular level confirm biochemical findings on the biosynthesis of calsequestrin and the ATPase. Immunofluorescent staining of myoblasts showed that calsequestrin first appears in a well-defined region of the cell near one end of the nucleus. At later times, the staining occupied progressively larger regions adjacent to the nucleus and took on a fibrous appearance. This suggests that calsequestrin first accumulates in the Golgi region and then gradually spreads throughout the cell. In contrast, the ATPase appeared to be concentrated in many small patches or foci throughout the cytoplasm and was never confined to one particular region, although some parts of the cell often stained more intensely than others. In multinucleated cells, alternating dark and fluorescent strands parallel to the longitudinal axis of the cells were evident.     

Role of cryptic genes in microbial evolution

Cryptic genes are phenotypically silent DNA sequences, not normally expressed during the life cycle of an individual. They may, however, be activated in a few individuals of a large population by mutation, recombination, insertion elements, or other genetic mechanisms. A consideration of the microbial literature concerning biochemical evolution, physiology, and taxonomy provides the basis for a hypothesis of microbial adaptation and evolution by mutational activation of cryptic genes. Evidence is presented, and a mathematical model is derived, indicating that powerful and biologically important mechanisms exist to prevent the loss of cryptic genes. We propose that cryptic genes persist as a vital element of the genetic repertoire, ready for recall by mutational activation in future generations. Cryptic genes provide a versatile endogenous genetic reservoir that enhances the adaptive potential of a species by a mechanism that is independent of genetic exchange.      

SplitsTree: analyzing and visualizing evolutionary data

MOTIVATION: Real evolutionary data often contain a number of different and sometimes conflicting phylogenetic signals, and thus do not always clearly support a unique tree. To address this problem, Bandelt and Dress (Adv. Math., 92, 47-05, 1992) developed the method of split decomposition. For ideal data, this method gives rise to a tree, whereas less ideal data are represented by a tree-like network that may indicate evidence for different and conflicting phylogenies. RESULTS: SplitsTree is an interactive program, for analyzing and visualizing evolutionary data, that implements this approach. It also supports a number of distances transformations, the computation of parsimony splits, spectral analysis and bootstrapping.